Zinc in PDB 7lps: Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)

The structure of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2), PDB code: 7lps was solved by R.P.Nowak, E.S.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	150.57 / 3.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	151.8, 117.292, 196.713, 90, 97.3, 90
R / Rfree (%)	28.9 / 30.3

The structure of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) (pdb code 7lps). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2), PDB code: 7lps:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:84.8 occ:1.00 SG B:CYS391 2.3 75.4 1.0 SG B:CYS394 2.3 99.5 1.0 SG B:CYS326 2.4 106.4 1.0 SG B:CYS323 2.6 111.5 1.0 CB B:CYS326 3.1 98.7 1.0 CB B:CYS391 3.1 77.2 1.0 CB B:CYS323 3.2 91.0 1.0 CB B:CYS394 3.5 95.1 1.0 N B:CYS394 3.8 88.0 1.0 N B:CYS326 3.9 104.1 1.0 CA B:CYS326 4.0 110.0 1.0 OG1 B:THR329 4.2 103.1 1.0 CA B:CYS394 4.2 87.1 1.0 CB B:THR329 4.3 95.9 1.0 CA B:CYS391 4.5 81.3 1.0 CG2 B:THR329 4.7 93.1 1.0 CA B:CYS323 4.7 87.2 1.0 CB B:ILE393 4.9 79.2 1.0 CB B:GLN325 4.9 100.6 1.0 C B:ILE393 4.9 92.2 1.0 C B:GLN325 4.9 100.0 1.0 N B:ILE393 5.0 80.2 1.0 C B:CYS394 5.0 92.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:95.7 occ:1.00 NE2 C:HIS162 2.0 100.0 1.0 SG C:CYS142 2.3 108.0 1.0 CE1 C:HIS162 2.3 105.1 1.0 SG C:CYS145 2.4 115.4 1.0 NE2 C:HIS158 2.5 106.9 1.0 CD2 C:HIS162 3.2 102.9 1.0 CB C:CYS145 3.3 115.7 1.0 CD2 C:HIS158 3.3 92.4 1.0 CB C:CYS142 3.4 100.1 1.0 N C:CYS145 3.4 111.0 1.0 CE1 C:HIS158 3.4 118.7 1.0 ND1 C:HIS162 3.5 107.3 1.0 CA C:CYS145 3.9 108.1 1.0 CG C:HIS162 3.9 108.1 1.0 CB C:GLN144 4.1 110.9 1.0 CG C:HIS158 4.4 90.8 1.0 C C:GLN144 4.4 113.9 1.0 ND1 C:HIS158 4.5 110.4 1.0 N C:GLY146 4.6 106.3 1.0 CA C:GLN144 4.6 109.1 1.0 C C:CYS145 4.7 106.6 1.0 CA C:CYS142 4.8 95.8 1.0 N C:GLN144 4.8 107.7 1.0 CB C:ALA147 4.8 97.3 1.0 CB B:HIS397 4.9 99.6 1.0 CG C:GLN144 5.0 111.3 1.0 O C:HIS158 5.0 109.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:87.3 occ:1.00 SG E:CYS394 2.2 101.4 1.0 SG E:CYS326 2.3 114.1 1.0 SG E:CYS391 2.3 86.2 1.0 SG E:CYS323 2.7 106.1 1.0 CB E:CYS326 3.1 108.3 1.0 CB E:CYS391 3.1 83.4 1.0 CB E:CYS394 3.3 101.3 1.0 CB E:CYS323 3.4 100.9 1.0 N E:CYS394 3.6 86.4 1.0 N E:CYS326 3.8 112.0 1.0 CA E:CYS326 4.0 120.9 1.0 CA E:CYS394 4.1 98.3 1.0 OG1 E:THR329 4.2 113.8 1.0 CB E:THR329 4.4 108.8 1.0 CA E:CYS391 4.6 92.6 1.0 C E:ILE393 4.8 86.7 1.0 CB E:ILE393 4.8 80.2 1.0 CB E:GLN325 4.8 116.0 1.0 C E:CYS394 4.8 98.1 1.0 CG2 E:THR329 4.9 109.1 1.0 CA E:CYS323 4.9 93.3 1.0 C E:GLN325 4.9 108.8 1.0 N E:ILE393 4.9 71.9 1.0 N E:ALA395 5.0 93.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:82.6 occ:1.00 NE2 F:HIS162 2.1 82.3 1.0 SG F:CYS142 2.2 77.2 1.0 NE2 F:HIS158 2.2 117.4 1.0 SG F:CYS145 2.5 100.8 1.0 CE1 F:HIS162 2.5 86.1 1.0 CD2 F:HIS158 3.0 116.7 1.0 CB F:CYS142 3.1 94.7 1.0 CE1 F:HIS158 3.2 117.5 1.0 CD2 F:HIS162 3.3 88.6 1.0 CB F:CYS145 3.4 86.5 1.0 N F:CYS145 3.6 84.4 1.0 ND1 F:HIS162 3.7 92.0 1.0 CA F:CYS145 4.1 84.6 1.0 CG F:HIS158 4.1 117.7 1.0 CG F:HIS162 4.1 94.8 1.0 ND1 F:HIS158 4.2 121.0 1.0 CB F:GLN144 4.4 83.7 1.0 CA F:CYS142 4.6 93.5 1.0 N F:GLY146 4.6 87.5 1.0 CB F:ALA147 4.6 97.5 1.0 C F:GLN144 4.6 80.8 1.0 C F:CYS145 4.8 85.7 1.0 N F:ALA147 4.8 96.0 1.0 CA F:GLN144 4.9 80.0 1.0 O F:HIS158 4.9 114.9 1.0 N F:GLN144 4.9 92.8 1.0 C F:CYS142 5.0 92.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn501 b:75.4 occ:1.00 CB H:CYS394 2.2 104.1 1.0 SG H:CYS391 2.4 84.2 1.0 SG H:CYS323 2.5 117.3 1.0 SG H:CYS326 2.8 105.8 1.0 SG H:CYS394 3.0 149.9 1.0 CB H:CYS391 3.0 86.1 1.0 CA H:CYS394 3.4 96.8 1.0 CB H:CYS326 3.5 97.1 1.0 CB H:CYS323 3.5 88.7 1.0 N H:CYS394 3.6 91.2 1.0 N H:CYS326 3.8 107.9 1.0 CA H:CYS326 4.2 104.5 1.0 CB H:GLN325 4.4 96.4 1.0 C H:CYS394 4.4 100.1 1.0 CA H:CYS391 4.5 89.0 1.0 OG H:SER396 4.6 118.6 1.0 CB H:SER396 4.6 103.1 1.0 N H:ALA395 4.6 99.2 1.0 C H:GLN325 4.7 103.8 1.0 N H:SER396 4.8 107.2 1.0 C H:ILE393 4.8 96.7 1.0 OG1 H:THR329 4.9 115.4 1.0 CA H:GLN325 5.0 97.4 1.0 CA H:CYS323 5.0 87.5 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:95.6 occ:1.00 NE2 I:HIS162 1.9 79.6 1.0 CE1 I:HIS162 2.3 88.7 1.0 SG I:CYS142 2.4 97.7 1.0 NE2 I:HIS158 2.4 95.0 1.0 SG I:CYS145 2.5 85.1 1.0 CD2 I:HIS162 3.2 83.5 1.0 CD2 I:HIS158 3.2 85.5 1.0 CE1 I:HIS158 3.3 106.9 1.0 CB I:CYS145 3.3 99.1 1.0 CB I:CYS142 3.4 90.5 1.0 ND1 I:HIS162 3.5 95.0 1.0 N I:CYS145 3.6 86.7 1.0 CG I:HIS162 3.9 86.8 1.0 CA I:CYS145 4.0 100.2 1.0 CB I:GLN144 4.2 97.3 1.0 CG I:HIS158 4.2 98.3 1.0 ND1 I:HIS158 4.3 113.7 1.0 C I:GLN144 4.5 89.1 1.0 N I:GLY146 4.7 97.3 1.0 CA I:GLN144 4.8 99.3 1.0 CA I:CYS142 4.8 85.5 1.0 CB I:ALA147 4.8 95.0 1.0 C I:CYS145 4.8 97.1 1.0 O I:HIS158 4.9 119.3 1.0 N I:GLN144 4.9 106.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn1001 b:89.2 occ:1.00 SG K:CYS394 2.2 82.1 1.0 SG K:CYS391 2.2 88.1 1.0 SG K:CYS326 2.3 94.3 1.0 SG K:CYS323 2.7 86.6 1.0 CB K:CYS326 3.1 98.0 1.0 CB K:CYS391 3.1 83.9 1.0 CB K:CYS394 3.3 87.0 1.0 CB K:CYS323 3.4 89.7 1.0 N K:CYS394 3.6 79.8 1.0 N K:CYS326 3.8 93.8 1.0 CA K:CYS326 4.0 103.0 1.0 CA K:CYS394 4.0 86.7 1.0 OG1 K:THR329 4.3 100.6 1.0 CB K:THR329 4.4 98.8 1.0 CA K:CYS391 4.6 93.6 1.0 C K:ILE393 4.7 83.3 1.0 CB K:ILE393 4.8 72.5 1.0 CB K:GLN325 4.8 105.7 1.0 C K:CYS394 4.8 83.7 1.0 CG2 K:THR329 4.8 98.5 1.0 CA K:CYS323 4.9 84.7 1.0 C K:GLN325 4.9 94.6 1.0 N K:ILE393 4.9 71.5 1.0 N K:ALA395 5.0 82.3 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of DDB1-Crbn-ALV1 Complex Bound to Helios (IKZF2 ZF2) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn201 b:83.7 occ:1.00 SG L:CYS145 2.2 100.0 1.0 SG L:CYS142 2.2 79.0 1.0 NE2 L:HIS162 2.3 86.5 1.0 NE2 L:HIS158 2.4 89.6 1.0 CE1 L:HIS162 2.7 88.6 1.0 CB L:CYS142 3.1 97.0 1.0 CB L:CYS145 3.1 100.3 1.0 CD2 L:HIS158 3.2 95.3 1.0 N L:CYS145 3.3 97.2 1.0 CE1 L:HIS158 3.4 91.7 1.0 CD2 L:HIS162 3.5 95.3 1.0 CA L:CYS145 3.7 98.9 1.0 ND1 L:HIS162 3.9 93.9 1.0 CB L:GLN144 4.2 105.4 1.0 N L:GLY146 4.3 98.7 1.0 CG L:HIS162 4.3 98.6 1.0 C L:GLN144 4.3 91.7 1.0 CG L:HIS158 4.3 96.4 1.0 ND1 L:HIS158 4.5 95.1 1.0 C L:CYS145 4.5 97.0 1.0 CB L:ALA147 4.5 98.9 1.0 CA L:CYS142 4.5 96.0 1.0 N L:ALA147 4.6 89.8 1.0 CA L:GLN144 4.6 99.4 1.0 N L:GLN144 4.7 103.4 1.0 CG L:GLN144 4.8 106.0 1.0 C L:CYS142 4.8 91.6 1.0 O L:CYS142 4.9 93.5 1.0

E.S.Wang, A.L.Verano, R.P.Nowak, J.C.Yuan, K.A.Donovan, N.A.Eleuteri, H.Yue, K.H.Ngo, P.H.Lizotte, P.C.Gokhale, N.S.Gray, E.S.Fischer. Acute Pharmacological Degradation of Helios Destabilizes Regulatory T Cells Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-021-00802-W